A very powerful feature of the SeqWord Genome Browser is that
it can be run locally on your
computer in a web browser. Data is
derived from an input sequence using OligoWords, or data exported and saved from the main web database, then results can be
simply viewed
using a web browser. In this way you can check your newly sequenced
genome or any fasta format sequence, such as newly sequenced plasmids
or genomic islands.

Requirements - A sequence in fasta
or GenBank format - The two packages from the website - The Java runtime environment with browser plugin
(version 5 (1.5) or later) - Python version 2.5Instructions

1 Obtaining data with OligoWordsPlace
your genome of interest in fasta (.fst, .fas, .fna) or GenBank (.gbk) format in the OligoWords input
directory, or use the provided plasmid pKLC102.fst example already in the directory.

Run OligoWords by double clicking OligoWords1.2.1.exe

The following window should appear:

Here you can change the list of Tasks to be carried out, and also the length and step of the sliding window.

To change the task list, type 't' and press 'Enter'. New menu will appear that allows you to
add or remove tasks from the list. Type 'a' to add a new task and then
type 'c' to select task category:

*generalized means that the expected frequency of
nucleotides will be normalized by frequencies of constutuent oligonucleotides
calculated for the complete genome rather than for a given sliding window (default).

Next select the scheme of normalization ('n') and the word length ('w'),
and type 'a', 'q' and 'q' followed by pressing 'Enter'
in three subsequent menus. You'll end up with the
first menu (see above). Type 'y' then Enter to start OligoWords.
OligoWords will process the fasta/Genbank files in the input directory. The output
is plain text files with the extension '.out' in the
output directory.
The number of output files will be the same as the number of input sequences. Note:
to ensure reliability of statistical calculations keep in mind that the sliding
window length should not be shorter than the following limits. These are set in relation to the maximum word length value.

Word length (bp)

Minimum sliding window size (bp)

2

300

3

1200

4

5000

5

18500

6

74000

7

295000

If the word length set for one task requires a larger sliding window, the
program will perform calculations as it is set without any warnings, but the
resulting values will be statistically unreliable!

2 Viewing output files with the SeqWord Genome Browser locally

To
view an output file use the on-line version of the SeqWord Genome Browser or a
local version of the applet MhhViewer.html (with associated Java jar file) which is freely available for download.
If you use the local applet, open it with your webbrowser and
allow the browser to display the applet by accepting the certificate if prompted.

Select File > Open and navigate to the OligoWords output folder to select the results of interest (image below)

Now you can view and analyse your results just like in the server version of the SeqWord Genome Browser.Gene
names and positions are of course not provided if you only use a fasta
sequence, since no annotation exists for the genome with this file type.